[Platform]: Add directionality column to coloc widgets (#572)

opentargets · Nov 28, 2024 · 8f61c66 · 8f61c66
1 parent 92f61c7
commit 8f61c66
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Showing 4 changed files with 79 additions and 3 deletions.
diff --git a/packages/sections/src/credibleSet/GWASColoc/Body.tsx b/packages/sections/src/credibleSet/GWASColoc/Body.tsx
@@ -1,5 +1,12 @@
 import { useQuery } from "@apollo/client";
-import { Link, SectionItem, DisplayVariantId, ScientificNotation, OtTable } from "ui";
+import {
+  Link,
+  SectionItem,
+  DisplayVariantId,
+  ScientificNotation,
+  OtTable,
+  Tooltip,
+} from "ui";
 import { naLabel } from "../../constants";
 import { definition } from ".";
 import Description from "./Description";
@@ -114,6 +121,36 @@ const columns = [
     id: "colocalisationMethod",
     label: "Colocalisation Method",
   },
+  {
+    id: "betaRatioSignAverage",
+    label: "Directionality",
+    tooltip: "Effect directionality based on the ratio of betas between the two credible sets",
+    renderCell: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return naLabel;
+      let category = "Inconclusive";
+      if (betaRatioSignAverage <= -0.99) category = "Opposite";
+      else if (betaRatioSignAverage >= 0.99) category = "Same";
+      const displayValue = Math.abs(betaRatioSignAverage) === 1
+        ? betaRatioSignAverage
+        : betaRatioSignAverage.toFixed(2)
+      return <Tooltip title={`Beta ratio sign average: ${displayValue}`}>
+        {category}
+      </Tooltip>
+    },
+    filterValue: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return null;
+      if (betaRatioSignAverage <= -0.99) return "Opposite";
+      else if (betaRatioSignAverage >= 0.99) return "Same";
+      return "Inconclusive";
+    },
+    sortable: false,
+    exportValue: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return null;
+      if (betaRatioSignAverage <= -0.99) return "Opposite";
+      else if (betaRatioSignAverage >= 0.99) return "Same";
+      return "Inconclusive";
+    },
+  },
   {
     id: "h3",
     label: "H3",

diff --git a/packages/sections/src/credibleSet/GWASColoc/GWASColocQuery.gql b/packages/sections/src/credibleSet/GWASColoc/GWASColocQuery.gql
@@ -24,6 +24,7 @@ query GWASColocQuery($studyLocusId: String!) {
       h3
       h4
       clpp
+      betaRatioSignAverage
     }
   }
 }
diff --git a/packages/sections/src/credibleSet/GWASMolQTL/Body.tsx b/packages/sections/src/credibleSet/GWASMolQTL/Body.tsx
@@ -1,5 +1,12 @@
 import { useQuery } from "@apollo/client";
-import { Link, SectionItem, DisplayVariantId, ScientificNotation, OtTable } from "ui";
+import {
+  Link,
+  SectionItem,
+  DisplayVariantId,
+  ScientificNotation,
+  OtTable,
+  Tooltip,
+} from "ui";
 import { naLabel } from "../../constants";
 import { definition } from ".";
 import Description from "./Description";
@@ -16,7 +23,7 @@ const columns = [
     label: "Navigate",
     renderCell: ({ otherStudyLocus }) => {
       if (!otherStudyLocus?.variant) return naLabel;
-      return(<Box sx={{ display: "flex" }}>
+      return (<Box sx={{ display: "flex" }}>
         <Link to={`./${otherStudyLocus.studyLocusId}`}>
           <FontAwesomeIcon icon={faArrowRightToBracket} />
         </Link>
@@ -132,6 +139,36 @@ const columns = [
     id: "colocalisationMethod",
     label: "Colocalisation Method",
   },
+  {
+    id: "betaRatioSignAverage",
+    label: "Directionality",
+    tooltip: "Effect directionality based on the ratio of betas between the two credible sets",
+    renderCell: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return naLabel;
+      let category = "Inconclusive";
+      if (betaRatioSignAverage <= -0.99) category = "Opposite";
+      else if (betaRatioSignAverage >= 0.99) category = "Same";
+      const displayValue = Math.abs(betaRatioSignAverage) === 1
+        ? betaRatioSignAverage
+        : betaRatioSignAverage.toFixed(2)
+      return <Tooltip title={`Beta ratio sign average: ${displayValue}`}>
+        {category}
+      </Tooltip>
+    },
+    filterValue: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return null;
+      if (betaRatioSignAverage <= -0.99) return "Opposite";
+      else if (betaRatioSignAverage >= 0.99) return "Same";
+      return "Inconclusive";
+    },
+    sortable: false,
+    exportValue: ({ betaRatioSignAverage }) => {
+      if (betaRatioSignAverage == null) return null;
+      if (betaRatioSignAverage <= -0.99) return "Opposite";
+      else if (betaRatioSignAverage >= 0.99) return "Same";
+      return "Inconclusive";
+    },
+  },
   {
     id: "h3",
     label: "H3",

diff --git a/packages/sections/src/credibleSet/GWASMolQTL/GWASMolQTLColocQuery.gql b/packages/sections/src/credibleSet/GWASMolQTL/GWASMolQTLColocQuery.gql
@@ -34,6 +34,7 @@ query GWASMolQTLColocQuery($studyLocusId: String!) {
       h3
       h4
       clpp
+      betaRatioSignAverage
     }
   }
 }